Update calculate_stability usage

[sjspielman]

Closes #870
Pretty much does what it says, following AlexsLemonade/rOpenScPCA#4!
Files were styled by pre-commit, too.

[sjspielman]

I did retrigger this run after the rOpenScPCA update went in, but maybe the environment was cached.

[sjspielman]

Environment indeed seems to be cached. Let's just re-trigger after the weekend!

[sjspielman]

Still mostly cached, but there was this line which makes me think rOpenScPCA was not cached, in which case I do not really understand why the updated rOpenScPCA wasn't retrieved. @jashapiro, do you have any ideas?

Installing rOpenScPCA ...      OK [built from source and cached in 20s]

[jashapiro]

Still mostly cached, but there was this line which makes me think rOpenScPCA was not cached, in which case I do not really understand why the updated rOpenScPCA wasn't retrieved. @jashapiro, do you have any ideas?

Installing rOpenScPCA ...      OK [built from source and cached in 20s]

Did you update renv.lock? It does record the commit hash, so I would expect that it is using that to retrieve the correct version.

[sjspielman]

Did you update renv.lock? It does record the commit hash, so I would expect that it is using that to retrieve the correct version.

Ah, I had assumed since we didn't do release/tag (though, we probably need to adopt a development branch over there...) that wouldn't change. Perhaps bad assumption..

[jashapiro]

we probably need to adopt a development branch over there...

I don't think that we do, at least not at this time.

[sjspielman]

When I snapshot'ed analyses/cell-type-ETP-ALL-03/renv.lock, a bunch of new packages got added. I guess it just had missed a snapshot in there at some point during development, but not enough to affect CI...?

[jashapiro]

Did you make this update manually, installing the commit directly? I would have expected the RemoteRef to stay as main, which will enable future updates with just renv::update("rOpenScPCA"). Otherwise we have to keep track of the hashes much more manually, which is annoying.

[sjspielman]

I did renv::install("rOpenScPCA@......"). Will go again with update

[jashapiro]

You should be able to just change these lines manually.

Suggested change

	"RemoteRef": "f71a8191130fa543e6506c73c7b62ffa55e8ba3f",
	"RemoteRef": "main",

[jashapiro]

LGTM